The congregation of St Mary's in Fernyhalgh Lane, close to the Ladyewell Shrine, called in a design company to address wet rot in the flooring of the church's sanctuary.
But suggestions put forward have failed to get approval from the city council.
Now it could mean parishioners going back to the drawing board to look at alternative ways of addressing the problem.
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Designers recommended removing rotted timber floorboards in the 228-year-old Catholic church and replacing them with new stone steps with under-floor heating.
The plan also involved removing the existing carpet and replacing it with a stone flag finish.
The church’s sanctuary has one step up to a raised timber platform and then a further two steps which are carpeted to the high altar.
"This surface material has been affected by wet rot and is now failing as a floor covering. It is stained and unsightly,” says a report to the council.
"Currently the raised timber platform to both levels doesn't have any ventilation.
"The timber joists to the lower sub-floor are resting on compacted ground and a number of joists are rotten and need replacement.
"The same can be said of the high altar sub-floor which is also of timber construction without ventilation."
The design will now go back to the scheme's agent, Peter O'Brien of the North West Historic Churches Committee, to review.
Fernyhalgh has been a sacred place of devotion for Catholics since the 11th century.
St Mary's was built in 1794 to cater for pilgrims who visited the Ladyewell Shrine just down the lane.